Heavy rain and flooding forced some rail services in and out of Birmingham to be cancelled.
Virgin West Coast had earlier not been stopping at the Birmingham stations, but the lines from Wolverhampton to Coventry reopened during rush hour.
The line near Water Orton, Warwickshire, was under several feet of water, which earlier affected services from Birmingham to the East Midlands.
There are six flood warnings in place across Staffordshire and Warwickshire.
They are on the River Tame from Water Orton to Lea Marston, the River Anker from Nuneaton to Tamworth and the River Cole from Shard End to Coleshill.
The River Avon, between Stratford-upon-Avon, Warwick and Rugby and the Stour in Kinver.
The Water Orton incident affected Virgin Cross Country services between Birmingham, the East Midlands and the North East, and Central Trains services between Birmingham and the East Midlands.
Central Trains has suspended its services from Birmingham to Walsall, Rugeley to Hednesford and Birmingham to Leicester.
Other services are running but are subject to delays and disruption.
River burst
But the line from Wolverhampton through Birmingham to Coventry reopened at about 0800 BST.
The Cross City Line North, from Redditch through Birmingham to Sutton Coldfield and Lichfield, is running again but with a half-hourly service.
About 100 people were trapped in a factory after a nearby river burst its banks and flooded the ground floor.
Water around the plant in Water Orton Lane, in Minworth, Sutton Coldfield, rose to about 6ft (1.83m) deep in places after the River Tame burst.
In Warwickshire parts of Leamington Spa have been affected with a number of businesses saying they would be closed on Friday.
Residents had to push several cars out of the water in the village of Cubbington.
A number of roads were also closed in Shirley and Solihull town centre.
A driver was trapped in the wreckage of his car for more than 30 minutes after a crash on the M42.
Ambulance crews found a car on its roof on the hard shoulder when they arrived at the scene between Junction 3a and 3 westbound.
The man had suffered a broken right leg and a chest injury.
In Worcestershire, roads in Kidderminster have been affected by flash flooding and the town's fire station has been hit by lightning, putting its emergency call system out of action. Several hundred houses have also been without power.
Flooding on the M40 near Gaydon on Thursday evening forced the closure of Warwick Services.
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